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opencc-by-nc-sa-4.0Jul 2023View details →

Supplementary data (CC BY-NC-SA 4.0): A reactive neural network framework for water-loaded acidic zeolites

Content (Creative Commons Attribution Non Commercial Share Alike 4.0 International):This dataset provides supplementary data to "A reactive neural network framework for water-loaded acidic zeolites". It contains trained Neural Network Potentials (NNP and ΔNNP model), scripts, and all energy and force data used in this work at the (Δ)NNP, ReaxFF, and DFT (SCAN+D3(BJ) and ωB97X-D3(BJ)) level. Energy and forces are stored as ASE trajectory files (traj), readable by the <a href="https://wiki.fysik.dtu.dk/ase/index.html">Atomic Simulation Environment </a>(ASE). In addition, this repository contains the generated training database with DFT (SCAN+D3(BJ)) energies and forces as SchNetPack1.0 database (SiAlOH.db) file readable by ASE and <a href="https://github.com/atomistic-machine-learning/schnetpack/tree/schnetpack1.0">SchNetPack version 1.0</a>.<ol><li>"aimd_simulations.zip" - VASP INCAR file, XDATCAR and traj file for 10 ps AIMD run (Supplementary Figure 6) and NNP level (re-)calculated energies/forces ("aimd_nnp_recalc.traj")</li><li>"biased_dynamics.zip" - VASP/Plumed input and output files for DFT (SCAN+D3(BJ)) and NNP level biased dynamics including traj files (Supplementary Figure 12)</li><li>"database_input.zip" - structure (cif) files of the initial structures used for database generation (Supplementary Table 1)</li><li>"delta_nnp.zip" - (pytorch) ΔNNP model (compatible with <a href="https://github.com/atomistic-machine-learning/schnetpack/tree/schnetpack1.0">SchNetPack version 1.0</a>) together with example scripts </li><li>"error_stats.zip" - traj files of all generalization tests (Figure 1 and Supplementary Figure 4) storing energies/forces at the SCAN+D3(BJ), ReaxFF, and NNP level as well as traj files with ΔNNP and ωB97X-D3(BJ) energies/forces for a subset taken from biased dynamics runs (Supplementary Figure 11)</li><li>"md_simulations.zip" - NNP level MD trajectories of all generalization test (Figure 1 and Supplementary Figure 4) runs including an example script for an MD run</li><li>"neb_calculations.zip" - traj files and example scripts for NEB calculations at the (Δ)NNP along with the corresponding DFT energy/force data (SCAN+D3(BJ) and ωB97X-D3(BJ))</li><li>"nnps.zip" - (pytorch) NNP model files (compatible with <a href="https://github.com/atomistic-machine-learning/schnetpack/tree/schnetpack1.0">SchNetPack version 1.0</a>)</li><li>"silica_database.zip" - output files of the single-point (SP) and optimization test runs (Supplementary Figure 1) of pure silica structures together with an example structure optimization script </li><li>"SiAlOH.db" - DFT (SCAN+D3(BJ)) training database as SchNetPack1.0 database file readable by ASE and <a href="https://github.com/atomistic-machine-learning/schnetpack/tree/schnetpack1.0">SchNetPack version 1.0</a></li></ol>

opencc-by-4.0Jan 2022View details →

Supplementary data: Accurate large-scale simulations of siliceous zeolites by neural network potentials

Content 1. Zeolite databases <ul> <li>Deem database containing 331170 hypothetical zeolite frameworks [Deem09, Pophale11] geometrically optimized at the NNPscan level (note, the first row of the database is alpha-quartz): "DEEM_NNPscan.db"</li> <li>Database of 236 exiting zeolite frameworks of the <a href="http://www.iza-structure.org/databases/">International Zeolite Association (IZA) </a>optimized at the NNPscan level: "IZA_NNPscan.db"</li> <li>Both databases are <a href="https://wiki.fysik.dtu.dk/ase/ase/db/db.html">ASE SQLite database files</a> of the <a href="https://wiki.fysik.dtu.dk/ase/index.html">Atomic Simulation Environment</a> containing the ASE <a href="https://wiki.fysik.dtu.dk/ase/ase/atoms.html">Atoms objects</a> with energies and forces (NNPscan level); readable with ASE's <a href="https://wiki.fysik.dtu.dk/ase/ase/io/io.html">I/O module</a></li> <li>Additionally, relevant quantities can be extracted with, e.g., the following queries (further information: ase db --help):</li> </ul> <pre><code class="language-bash">ase db DEEM_NNPscan.db -c id,formula,natoms,volume,mass,density,energy_per_tsite,n_tsites,relative_energy # Output id|formula|natoms| volume| mass|density|energy_per_tsite|n_tsites|relative_energy 1|O6Si3 | 9|111.161|180.249| 26.988| -31.796| 3| 0.000 2|O16Si8 | 24|433.858|480.664| 18.439| -31.638| 8| 15.265 3|O16Si8 | 24|421.114|480.664| 18.997| -31.596| 8| 19.359 4|O16Si8 | 24|426.557|480.664| 18.755| -31.614| 8| 17.613 5|O16Si8 | 24|412.410|480.664| 19.398| -31.613| 8| 17.677 6|O16Si8 | 24|393.544|480.664| 20.328| -31.594| 8| 19.546 7|O16Si8 | 24|422.400|480.664| 18.939| -31.657| 8| 13.476 8|O16Si8 | 24|394.405|480.664| 20.284| -31.581| 8| 20.797 9|O12Si6 | 18|265.201|360.498| 22.624| -31.611| 6| 17.868 10|O16Si8 | 24|357.047|480.664| 22.406| -31.581| 8| 20.785 11|O16Si8 | 24|434.894|480.664| 18.395| -31.621| 8| 16.911 12|O16Si8 | 24|384.158|480.664| 20.825| -31.657| 8| 13.448 13|O12Si6 | 18|258.977|360.498| 23.168| -31.679| 6| 11.278 14|O16Si8 | 24|466.429|480.664| 17.152| -31.593| 8| 19.588 15|O16Si8 | 24|423.469|480.664| 18.892| -31.639| 8| 15.179 16|O16Si8 | 24|450.716|480.664| 17.750| -31.628| 8| 16.219 17|O16Si8 | 24|331.528|480.664| 24.131| -31.642| 8| 14.857 18|O16Si8 | 24|458.573|480.664| 17.445| -31.635| 8| 15.572 19|O16Si8 | 24|359.298|480.664| 22.266| -31.655| 8| 13.636 20|O16Si8 | 24|464.264|480.664| 17.232| -31.612| 8| 17.750 Rows: 331171 (showing first 20) Keys: density, energy_per_tsite, n_tsites, relative_energy ase db IZA_NNPscan.db -c id,formula,natoms,volume,mass,density,energy_per_tsite,n_tsites,relative_energy,iza_code # Output id|formula |natoms| volume| mass|density|energy_per_tsite|n_tsites|relative_energy|iza_code 1|O16Si8 | 24| 435.488| 480.664| 18.370| -31.676| 8| 11.594|ABW 2|O32Si16 | 48| 961.419| 961.328| 16.642| -31.645| 16| 14.612|ACO 3|O96Si48 | 144|3154.579|2883.984| 15.216| -31.664| 48| 12.810|AEI 4|O80Si40 | 120|2102.921|2403.320| 19.021| -31.703| 40| 9.021|AEL 5|O96Si48 | 144|2417.286|2883.984| 19.857| -31.666| 48| 12.586|AEN 6|O144Si72| 216|4075.300|4325.976| 17.667| -31.674| 72| 11.831|AET 7|O96Si48 | 144|2786.810|2883.984| 17.224| -31.675| 48| 11.716|AFG 8|O48Si24 | 72|1400.247|1441.992| 17.140| -31.690| 24| 10.268|AFI 9|O64Si32 | 96|1764.823|1922.656| 18.132| -31.653| 32| 13.809|AFN 10|O80Si40 | 120|2080.330|2403.320| 19.228| -31.707| 40| 8.632|AFO 11|O64Si32 | 96|2097.384|1922.656| 15.257| -31.655| 32| 13.622|AFR 12|O112Si56| 168|3820.116|3364.648| 14.659| -31.650| 56| 14.150|AFS 13|O144Si72| 216|4732.720|4325.976| 15.213| -31.664| 72| 12.793|AFT 14|O60Si30 | 90|1897.074|1802.490| 15.814| -31.659| 30| 13.268|AFV 15|O96Si48 | 144|3154.885|2883.984| 15.214| -31.664| 48| 12.776|AFX 16|O32Si16 | 48|1137.335| 961.328| 14.068| -31.591| 16| 19.790|AFY 17|O48Si24 | 72|1283.812|1441.992| 18.694| -31.620| 24| 17.034|AHT 18|O96Si48 | 144|2479.287|2883.984| 19.360| -31.681| 48| 11.155|ANA 19|O64Si32 | 96|1797.086|1922.656| 17.807| -31.662| 32| 12.924|APC 20|O64Si32 | 96|1751.393|1922.656| 18.271| -31.678| 32| 11.422|APD Rows: 236 (showing first 20) Keys: density, energy_per_tsite, iza_code, n_tsites, relative_energy # Filtering of the database, e.g., for structures with relative energies < 10 kJ/(mol Si) ase db IZA_NNPscan.db relative_energy\<10 -c density,energy_per_tsite,n_tsites,relative_energy,iza_code # Output density|energy_per_tsite|n_tsites|relative_energy|iza_code 19.021| -31.703| 40| 9.021|AEL 19.228| -31.707| 40| 8.632|AFO 19.385| -31.695| 24| 9.802|ATV 18.778| -31.702| 34| 9.061|DOH 19.570| -31.693| 24| 9.959|EWO 18.401| -31.698| 32| 9.451|GON 18.551| -31.695| 112| 9.807|IHW 17.778| -31.693| 288| 9.972|IMF 19.154| -31.695| 6| 9.762|JBW 18.187| -31.695| 96| 9.734|MFI 19.278| -31.709| 48| 8.443|MRE 18.035| -31.698| 90| 9.481|MSO 20.417| -31.724| 44| 7.003|MTF 19.227| -31.704| 136| 8.898|MTN 18.542| -31.693| 28| 9.966|MTW 19.137| -31.695| 60| 9.798|PCR 20.037| -31.709| 144| 8.464|PSI 18.843| -31.703| 64| 9.004|SAF 18.371| -31.703| 112| 8.975|STO 19.894| -31.706| 17| 8.671|VET Rows: 20 (showing first 20) Keys: density, energy_per_tsite, iza_code, n_tsites, relative_energy</code></pre> <ul> <li>The quantities shown above are available with the keys (besides standard ASE database keys):</li> </ul> <table> <thead> <tr> <th scope="col">Key</th> <th scope="col">Quantity</th> <th scope="col">Unit</th> </tr> </thead> <tbody> <tr> <td>id</td> <td>Identifier</td> <td> </td> </tr> <tr> <td>formula</td> <td>Chemical formula of the unit cell</td> <td> </td> </tr> <tr> <td>natoms</td> <td>Number of atoms</td> <td> </td> </tr> <tr> <td>volume</td> <td>Unti cell volume</td> <td>Å3</td> </tr> <tr> <td>mass</td> <td>Atomic mass of the unit cell</td> <td>amu</td> </tr> <tr> <td>density</td> <td>Framework density</td> <td>Si/nm3</td> </tr> <tr> <td>energy_per_tsite</td> <td>NNPscan energy</td> <td>eV</td> </tr> <tr> <td>n_tsites</td> <td>Number of T-sites</td> <td> </td> </tr> <tr> <td>relative_energy</td> <td>Energy with respect to quartz</td> <td>kJ/(mol Si)</td> </tr> <tr> <td>iza_code</td> <td>only for 'IZA_NNPscan.db'</td> <td> </td> </tr> </tbody> </table> <ul> <li> Comma separated csv files for the quantities listed above: "DEEM_NNPscan.csv" and  "IZA_NNPscan.csv"</li> </ul> 2. Neural network potentials (NNP) for silica <ul> <li>SchNet [Schütt18,Schütt19] NNP files trained on DFT data at the PBE+D3 (NNPpbe) and SCAN+D3 level (NNPscan)</li> <li>Simulations can be performed using <a href="https://schnetpack.readthedocs.io/en/stable/getstarted/getstarted.html#references">SchNetPack</a> with its ASE calculator</li> <li>This example shows a simple single-point calculation</li> </ul> <pre><code class="language-python">import ase.io import torch from schnetpack.interfaces import SpkCalculator from schnetpack.environment import AseEnvironmentProvider # check if GPU(s) are available if torch.cuda.is_available(): device = "cuda" else: device = "cpu" # load the NNP model model = torch.load('SiOscan1', map_location=device) # read some structure atoms = ase.io.read( ... ) # define SchNetPack calculator calc = SpkCalculator(model=model, device=device, energy='energy', forces='forces', environment_provider=AseEnvironmentProvider(6.) ) # attach calculator to atoms object atoms.set_calculator(calc) # perform simulations, e.g., single-point calculation energy = atoms.get_potential_energy() print(energy)</code></pre> 3. Test set used for accuracy evaluation (ASE database: test_set_NNPscan.db)

opencc-by-4.0Oct 2022View details →

Zeolite Templated Carbon Materials - DFTB Structural Database

Zeolite-templated carbon (ZTC) is a unique porous carbonaceous material in that its structure is ordered at the nanometre scale, enabling a representative periodic description at the atomistic level. A structural library for ZTC of varying compositions was created  using density functional tight binding (DFTB) potentials parameterized for materials science applications (matsci-0-3). We provide here  quantum chemical-refined structures of models with CH, CHO, CHON, CHOB, and CHOBN compositions with various degrees of heteroatom substitution. The "initial ZTC structure" files correspond to the initial model used in our work that was developed using molecular mechanics, empirical force fields. These structural models comprise the characteristic morphological features of highly porous carbon materials, such as open-blade surfaces, edges, saddles, and closed-strut formations, spanning a range of curvatures and characteristic sizes. The optimized structures in CIF and native DFTB file formats are organized in the "stationary structure" file based on the optimization pathways that lead to the stationary structures. Secondly, we carried out alternating compression and expansion of the CHO model unit cell to determine the lowest energy structure as well as to obtain the bulk modulus. The file "bulk modulus" contains two data sets that describe the deformational energy landscape of pure faujasite zeolite, Na-substituted zeolite, and the ZTC model structure. The file "analysis tools" is a representative compilation of utilities for file format conversion, fractional vs. Cartesian crystal coordinates, and structural analysis spreadsheets. The agreement between experimental measurements and the computational model is remarkable that demonstrates the power of approximate density functional theory as a cost-effective computational tool with chemical accuracy for the investigation of structure/property relationships in real-world carbon-based solids.

Zinc Doped Zeolite 13X DIAD X-Ray Computed Tomography - 0.54 micron pixel size RAW

This repository contains raw data for the zinc-doped zeolite 13X sample imaged on the DIAD beamline at Diamond Light Source. Data is stored as a .nxs file which can be loaded using ImageJ/Fiji. The size of this dataset is 2510x2510x2110 with a pixel-size of 0.54 microns. A script containing the savu process list and code used to perform the 3D reconstruction is provided. A detailed data descriptor pre-print can be found at https://arxiv.org/abs/2409.07322#   The size of the .h5 file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 43334_raw.h5 </blockquote> Please replace dataset_url with the url you copied.

Zinc Doped Zeolite 13X I13-2 X-Ray Computed Tomography - 1.625 micron pixel size

This repository contains data for the zinc-doped zeolite 13X sample imaged on the I13-2 beamline at Diamond Light Source. Data is stored as a .h5 file which can be loaded using ImageJ/Fiji. The size of this dataset is 2510x2510x2110 with a pixel-size of 1.625 microns. This data is one of four resolutions obtained. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322# The size of the .h5 file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 169067_recon.h5 </blockquote> Please replace dataset_url with the url you copied.

Zinc Doped Zeolite 13X DIAD X-Ray Computed Tomography - 0.54 micron pixel size

This repository contains processed data for the zinc-doped zeolite 13X sample imaged on the DIAD beamline at Diamond Light Source. Data is stored as a .nxs file which can be loaded using ImageJ/Fiji. The size of this dataset is 2510x2510x2110 with a pixel-size of 0.54 microns. A script containing the savu process list and code used to perform the 3D reconstruction is provided. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322# The size of the .h5 file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 43334_recon.h5 </blockquote> Please replace dataset_url with the url you copied.

Zinc Doped Zeolite 13X I13-2 X-Ray Computed Tomography - 0.325 micron pixel size

This repository contains data for the zinc-doped zeolite 13X sample imaged on the I13-2 beamline at Diamond Light Source. Data is stored as a .h5 file which can be loaded using ImageJ/Fiji. The size of this dataset is 2510x2510x2110 with a pixel-size of 0.325 microns. This data is one of four resolutions obtained. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322# The size of the .h5 file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 169065_recon.h5 </blockquote> Please replace dataset_url with the url you copied.

Zinc Doped Zeolite 13X I13-2 X-Ray Computed Tomography - 0.8125 micron pixel size

This repository contains data for the zinc-doped zeolite 13X sample imaged on the I13-2 beamline at Diamond Light Source. Data is stored as a .h5 file which can be loaded using ImageJ/Fiji. The size of this dataset is 2510x2510x2110 with a pixel-size of 0.8125 microns. This data is one of four resolutions obtained. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322# The size of the .h5 file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 169066_recon.h5 </blockquote> Please replace dataset_url with the url you copied.

Zinc Doped Zeolite 13X I13-2 X-Ray Computed Tomography - 2.6 micron pixel size

This repository contains data for the zinc-doped zeolite 13X sample imaged on the I13-2 beamline at Diamond Light Source. Data is stored as a .h5 file which can be loaded using ImageJ/Fiji. The size of this dataset is 2510x2510x2110 with a pixel-size of 2.6 microns. This data is one of four resolutions obtained. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322# The size of the .h5 file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 169068_recon.h5 </blockquote> Please replace dataset_url with the url you copied.

opencc-by-4.0Jul 2021View details →

17O-EPR determination of the structure and dynamics of copper single-metal sites in zeolites

Description of the dataset: <ul> <li>Data type: Experimental spectroscopic measurements, computer simulation and analysis</li> <li>Files are with filename extensions: DSC, DAT, spc, par, m, f34, xyz, out, in</li> <li>Information on origin of the data:</li> </ul> <ul> <li>EPR spectroscopic measurements with filename extensions DSC, DTA, spc and par.</li> <li>EPR spectroscopic simulation and analyses with filename extension m.</li> <li>Periodic DFT computations with(out) filename extensions out and f34 in ASCII format.</li> <li>Molecular cluster DFT computations with filename extensions in and out in ASCII format.</li> <li>Geometry information of cluster models is stored in xyz files in ASCII format.</li> </ul> <ul> <li>X-band CW-EPR spectroscopic measurements were generated by EMX spectrometer equipped with SHQ cavity produced by Bruker.</li> <li>Q-band and X-band Pulsed-EPR spectroscopic measurements were generated by ELEXYS 580 EPR spectrophotometer equipped with SHQ cavity and ER035 M NMR gaussmeter produced by Bruker.</li> <li>Periodic DFT computations were generated using distributed parallel version of CRYSTAL17 code.</li> <li>Molecular cluster DFT computations were generated using the ORCA (v4.2.1) code.</li> <li>If t <ul> <li>Files in PARACAT_WP3_20210625_01_CW folder includes X-band CW-EPR spectroscopic measurements; original data are in DTA/DSC and spc/par formats.</li> <li>Files in PARACAT_WP3_20210625_02_HYSCORE folder includes HYSCORE spectroscopic measurements; original data are in DTA/DSC formats.</li> <li>Files in PARACAT_WP3_20210625_03_ESE folder includes ESE spectroscopic measurements; original data are in DTA/DSC formats.</li> <li>Files in PARACAT_WP3_20210625_04_ENDOR folder includes ENDOR spectroscopic measurements; original data are in DTA/DSC formats.</li> <li>Files in PARACAT_WP3_20210625_05_MATLAB folder includes computer simulations/analyses of the EPR measurements; data are in m formats.</li> <li>Files in PARACAT_WP3_20210625_06_DFT folder includes periodic and cluster DFT computation inputs, outputs and geometries in ASCII format.</li> </ul> </li> </ul> <ul> <li>Information on: <ul> <li>specialized abbreviations: EPR – Electron Paramagnetic Resonance, CW – Continuous Wave EPR, ESE – Electron Spin Echo detected EPR, HYSCORE – HYperfine Sublevel CORrelation spectroscopy, ENDOR – Electron Nuclear DOuble Resonance spectroscopy, DFT – Density Functional Theory, CHA – Chabazite, zeolite topology.</li> <li>definitions of variables: Magnetic field, Temperature.</li> <li>units of measurement: Gauss (G), K, degree (°), milliTesla (mT).</li> <li>abbreviations: 6MR, 8MR are the Cu docking sites; 2Al-3NN, 2Al-2NN, 1Al are the different aluminium distributions analysed; 1w, 2w, 3w, 4w indicates the number of water ligands considered in the models; eq and ax indicates equatorial and axial ligands. Periodic DFT computations with filename extension .f34 include structural/symmetry information of optimized structure. Molecular cluster DFT computations with filename extension .in/.out/.xyz are inputs, outputs, and structure of cluster models.</li> </ul> </li> </ul>

opencc-by-4.0Sep 2022View details →

Assessing the Influence of Zeolite Composition on Oxygen-Bridged Diamino Dicopper(II) Complexes in Cu-CHA DeNOx Catalysts by Machine Learning-Assisted X‑ray Absorption Spectroscopy

<ul> <li>Data type: Experimental spectroscopic measurements and related elaboration from Figures 1-4 of the corresponding article</li> <li>Files are with filename extensions: txt</li> <li>Information on origin of the data:</li> </ul> In situ XANES and EXAFS data were collected at the BM23 beamline of the European Synchrotron Radiation Facility (ESRF, Grenoble, France) in a Microtomo reactor cell; measured Cu-CHA samples are indicated in the following with “Cu/Al”-“Si/Al” labels <ul> <li>fig_01_XANES: Normalized Cu K-edge XANES for Cu-CHA samples 0.1-5; 0.5-15; 0.6-29, collected at 200 °C after pretreatment in O2, reduction in NO+NH3 and subsequent oxidation in O2.</li> <li>fig_02_Conversion: NOx conversion in the 150−500 °C temperature range for Cu-CHA samples 0.1-5, 0.5-15, 0.6-29; TOF at 200 °C versus fraction of Cu(I) from XANES LCF after oxidation and fraction of Cu(I) from XANES LCF after oxidation versus Cu density for the same catalysts.</li> <li>fig_03_EXAFS_FT_WT: Magnitude of experimental EXAFS spectra, obtained by Fourier transforming k2χ(k) spectra in the 2.4−12.0 Å−1 range for Cu-CHA samples 0.1-5, 0.5-15, 0.6-29 after reduction in NO+NH3 and subsequent oxidation in O2; corresponding EXAFS WT maps magnified in high-R range (2-4 Å), obtained using a Morlet WT with parameters (σ=1, η=7).</li> <li>fig_04_EXAFS_MLfit: Magnitude of experimental and best fit EXAFS spectra, obtained by Fourier transforming k2χ(k) spectra in the 2.4−12.0 Å−1 range for Cu-CHA samples 0.1-5, 0.5-15, 0.6-29 after oxidation in O2. Scaled components 1 ([CuI(NH3)2]+), 2 and 3 (planar and bent μ-η2,η2-peroxo diamino dicopper(II)) isolated by ML-assisted EXAFS fitting are also reported, vertically translated.</li> <li>Information on:</li> <li>specialized abbreviations: CHA– chabazite; XANES– X-ray absorption near edge structure, EXAFS – Extended X-ray absorption fine structure; LCF – Linear Combination Fit; FT: Fourier Transform; WT – Wavelet Transform; ML – Machine Learning; TOF – Turn Over Frequency;</li> </ul>

opencc-by-4.0Jul 2018View details →

Continuous rotation electron diffraction data for Zeolite Mordenite

Raw continuous rotation electron diffraction data for mordenite:     - mordenite_cRED_1.zip     - mordenite_cRED_2.zip The zip file contains 3 directories          - SMV: Diffraction data (stretch correction applied) in SMV format     - Tiff: Raw diffraction data in 16-bit unsigned integer TIFF format     - Defocused images in 16-bit unsigned integer TIFF format Experimental parameters are stored in the header files of the SMV images, and in the file cRED_log.txt The SMV data can be processed using XDS. Raw serial electron diffraction data sets for mordenite:     - mordenite_SerialED.zip The zip file contains at least 3 directories:     - calib: contains the calibration files for the experiment     - data: contains the raw diffraction data for all the identified crystals in hdf5 format     - images: contains the image data used to locate crystals in hdf5 format Experimental parameters (such as the crystal coordinates) are stored in the attributes on the data files. The Python code to process the data can be found in the problematic-0.1.0.zip folder or on http://github.com/stefsmeets/problematic Prediction scores for all diffraction patterns are given in `learning.csv`

Zinc-doped Zeolite 13X, Partially Zinc-doped Zeolite 13X, and pure Zeolite 13X X-Ray Powder Diffraction

This repository holds X-Ray Powder Diffraction data for three different Zeolite 13X samples to allow for characterisation of the diffraction pattern for zinc-doped Zeolite 13X to perform accurate phase-based diffraction-tomography reconstructions using the data from 10.5281/zenodo.13329639. The three samples are fully Zinc-doped Zeolite 13X, partially Zinc-doped 13X, and pure Zeolite 13X. An empty borosilicate glass capillary is provided to remove scattering from the capillary the samples were housed in. Data in all instances is provided in ASCII format as a .asc file. A basic jupyter notebook is provided to perform the analysis used to determine powder peaks. Data was collected on a Rigaku SmartLab Diffractometer with a copper x-ray source of wavelength 1.5406 angstroms at the ISIS Neutron & Muon Source Materials Characterisation Lab. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322#

Zinc Doped Zeolite 13X I13-2 X-Ray Computed Tomography - 0.325 micron pixel size RAW

This repository contains raw data for the zinc-doped zeolite 13X sample imaged on the I13-2 beamline at Diamond Light Source. Raw data at a pixel-size of 0.325 microns is stored as a .nxs file, and a savu process list is provided to perform the reconstruction we used to reproduced the reconstructed data. This data is one of four resolutions obtained. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322# The size of the .hdf file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 169065_raw.hdf </blockquote> Please replace dataset_url with the url you copied.

Zinc Doped Zeolite 13X I13-2 X-Ray Computed Tomography - 1.625 micron pixel size RAW

This repository contains raw data for the zinc-doped zeolite 13X sample imaged on the I13-2 beamline at Diamond Light Source. Raw data at a pixel-size of 1.625 microns is stored as a .nxs file, and a savu process list is provided to perform the reconstruction we used to reproduced the reconstructed data. This data is one of four resolutions obtained. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322# The size of the .hdf file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 169067_raw.hdf </blockquote> Please replace dataset_url with the url you copied.

Zinc Doped Zeolite 13X I13-2 X-Ray Computed Tomography - 2.6 micron pixel size RAW

This repository contains raw data for the zinc-doped zeolite 13X sample imaged on the I13-2 beamline at Diamond Light Source. Raw data at a pixel-size of 2.6 microns is stored as a .nxs file, and a savu process list is provided to perform the reconstruction we used to reproduced the reconstructed data. This data is one of four resolutions obtained. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322# The size of the .hdf file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 169068_raw.hdf </blockquote> Please replace dataset_url with the url you copied.

Zinc Doped Zeolite 13X DIAD X-Ray Diffraction Computed Tomography - 25 and 50 micron spot-size

This repository contains X-Ray Diffraction Computed Tomography (XRD-CT) data of a zinc doped zeolite 13X sample on the Dual Imaging and Diffraction (DIAD / K11) at Diamond Light Source. XRD-CT data is provided at a diffraction spot size of 25 microns for three region of interest slices, with a dataset size of 40x2000x80. Both the raw and reconstructed data is provided, along with the code to perform the reconstructions.  XRD-CT data is also provided at a diffraction spot size of 50 microns for a full 1.05mm volume, with a dataset size of 20x2000x40. Scans start at 43336 and finish at 43401, with a movement of 0.05mm vertically upwards between each scan. The raw and reconstructed data is provided, along with the code used to perform the reconstructions. Note: Scan 43401 is excluded as a phase-based reconstruction could not be performed. Powder X-Ray Diffraction data can be found in an alternative repository at 10.5281/zenodo.13329670 which provides the q-values of the peaks for both the Zn and Na phase to allow the best reconstructions. A detailed data descriptor pre-print can be found at https://arxiv.org/abs/2409.07322

Zinc Doped Zeolite 13X I13-2 X-Ray Computed Tomography - 0.8125 micron pixel size RAW

This repository contains raw data for the zinc-doped zeolite 13X sample imaged on the I13-2 beamline at Diamond Light Source. Raw data at a pixel-size of 0.8125 microns is stored as a .nxs file, and a savu process list is provided to perform the reconstruction we used to reproduced the reconstructed data. This data is one of four resolutions obtained. A detailed data descriptor pre-print is available at https://arxiv.org/abs/2409.07322# The size of the .hdf file is >50GB and cannot be downloaded from the browser. It is recommended to use a terminal to download the data using the 'curl' or 'wget' command. To generate a file url, right-click the 'Download' button for the dataset you want to download and select 'Copy Link. Enter the following command in your terminal to download the dataset: <blockquote> curl dataset_url > 169066_raw.hdf </blockquote> Please replace dataset_url with the url you copied.